Default parameters for generation of synthetic data

Default parameters for generation of synthetic data

Usage

params_sc_synthetic_data(
  n_cells = 1000L,
  n_genes = 100L,
  n_batches = 1L,
  marker_genes = list(cell_type_1 = list(marker_genes = 0:9L), cell_type_2 =
    list(marker_genes = 10:19L), cell_type_3 = list(marker_genes = 20:29L)),
  batch_effect_strength = c("strong", "medium", "weak"),
  n_samples = NULL,
  sample_bias = NULL
)

Arguments

n_cells

Integer. Number of cells.

n_genes

Integer. Number of genes.

n_batches

Integer. Number of batches.

marker_genes

List. A nested list that indicates which gene indices are markers for which cell.

batch_effect_strength

String. One of c("strong", "medium", "weak"). The strength of the batch effect to add.

n_samples

Optional integer. Shall sample membership be added to the synthetic data. If you want sample information you need to provide n_samples and sample_bias.

sample_bias

Optional string. One of c("even", "slightly_uneven", "very_uneven")

Value

A list with the parameters.